Here are the rules. We start with a fully sorted deck of 52 cards, and we deal out four hands. We don’t deal in the ordinary way, either: we give the top 13 cards to the first player, then the next 13 to the second, and so forth. (We could also do the usual deal, but it makes the illustration and logic a little more difficult to see. We’ll keep it simple for now.)

This is what the table will look like.

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Next, we play the game, whatever it is. It really doesn’t matter, since we know exactly what hand everyone has, right? So don’t worry about the rules for that. What’s important is that next the dealer carefully picks up each hand in reverse order and stacks them, restoring the original arrangement of the deck.

Then he deals them out again in the same way. NO SHUFFLING! You don’t even get to cut the cards. The next round will look like this:

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Then repeat. Millions of times.

What did I tell you? The most boring card game in the universe. Well, other than 52 card pick-up…this one at least has a few simple rules, and probably the source of the boredom is simply the inflexibility of those rules.

What is the point of this exercise? It’s an analogy. Think of the deck of cards as a genome, with each card representing a single gene. Each hand is a chromosome, so in this example, we’re looking at an organism with 52 genes in 4 chromosomes. This particular game is what mitosis is like — each cell division is a precise, boring set of mechanical operations that make sure the same genes get distributed to each daughter cell. The rules guarantee that the same arrangement will get passed on from generation to generation.

Now, though, this leads to an interesting logic game. It’s supposed to be boring and repetitive, but what if the dealer and the hands are imperfect, and occasionally make a mistake? Not often, mind you, but every once in a while the hands are dealt out, and the distribution is different. We can have some fun with this — it’s a kind of detective game. Say the hands are dealt out, and you see this (hint: look at hand 3):

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You don’t actually get to see the event that occurred, but only the result. How would you explain what happened in the prior round? Try to come up with the simplest, minimal explanation.

Answer: it looks like some of the cards in hand 3, the 5-8 of diamonds, were reversed in order. That’s all, a simple change that we can logically decipher from the outcome. Note also that from now on, every round dealt out from this deck will propagate this new arrangement — we will always have that inversion in the diamonds, unless an accident rearranges them again. And to keep with the analogy, we see this in chromosomes too, small blocks of genes that get flipped around.

So we deal a few hundred thousand more hands, all looking the same, and then we notice something new. Figure out the simplest explanation for what happened here:

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A-ha, you should be saying, it looks like hand 2 swapped her last 5 cards with the last 5 cards that were dealt to hand 3. We also have an analogous process in genetics — it’s called a reciprocal translocation.

If we wanted to make this an even harder game, I could have given you that last set of hands and told you to compare it to the first, without showing you the intermediate inversion error. You’d still be able to figure out, though, that the simplest explanation was that there was an inversion and then a translocation, in that order, and we’d be able to puzzle out the series of slow, small accidents that generated this arrangement. (This won’t always be true: some combinations of rearrangements will be ambiguous and you’ll only be able to approximate what happened.)

We can also make it harder. There are plenty of genetic operations that can be tossed in: we can fuse two hands. We could split one hand so that now 5 hands at a time get dealt out. We can toss in duplications — maybe one of the players has an ace of hearts up his sleeve, and he slips it into the deck. Maybe someone tosses out the 2 of spades. The important thing is that these little distortions of the arrangement happen relatively rarely, leading to a slow rearrangement of the cards in the deck. There is nothing like a series of shuffles that scramble everything all at once.

This particular game is one that is played in comparative genomics all the time, only the magnitude of the complexity of the puzzle is much, much greater. We’re now dealing with tens of thousands of cards in a deck, in a series of rounds that have been played over hundreds of millions of years. The only thing that makes it possible to play is that the changes have been relatively slow — not every generation and not even every speciation event is accompanied by an error — and that, whatever the card game is that real species are playing, some arrangements of cards are advantageous and are conserved. The problem can be so difficult that not everything can be figured out, and what we often settle for is mapping out synteny.

And what, please, is synteny? Synteny is the conservation of blocks of order within two sets of chromosomes that are being compared. Let’s look at our original set of hands, and compare it to the set that was produced by an inversion and a translocation as a simple example.

Here’s the original, and I’ve added a little color coding to mark out the clusters of cards. Let’s call each set of cards a species, as a simple label.

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Now here’s the lightly scrambled round:

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Real genes aren’t nicely picked out with suit markings to make it easy to see how they are related, but what we see here in the background colors are blocks of conserved order. Those blocks are regions of synteny. For instance, the region in Hand 2 of Species 2 that contains the 7-8-4-3-2 of diamonds corresponds coarsely to a region of Hand 3 in Species 1 — it’s not perfect, because it’s missing the 5 and 6 of diamonds, and the 7 and 8 are reversed, but we can at least say there’s a kind of macro-synteny at play here, a larger block of rough correspondence with a whole chromosome. Within that syntenic region, there is some local scrambling, so if we wanted to go into more detail, we could say that the 7-8 of diamonds in Hand 2 preserve the micro-syntenic order of a piece of Hand 3 in Species 1, and the 4-3-2 of diamonds in Hand 2 are another micro-syntenic region conserved from Hand 3 of Species 1.

I know. It’s complicated, it’s got some weird terminology, and the logic can get convoluted…and this is a very simple example. In the real world of comparative genomics, you get much more elaborately scrambled examples, and you don’t get to see the ancestral species — you get two independently evolved species, and you have to puzzle out the minimal set of separate operations that would generate the two products, and infer the ancestral chromosomal arrangement from that. Computers are essential for working out the permutations.

In papers that describe synteny between two species, they’ll often do exactly what I illustrated above: they’ll color code the chromosomes from one species, and then map those regions of color onto the chromosomes of the other. Here’s one example:

There’s a key at the bottom. In this case, the authors have color-coded the 21 chromosomes of the puffer fish, Tetraodon — all the genes on chromosome 1 are colored dark purple, for instance, and all the genes on chromosome 9 are light blue. Then they look in the human genome, and wherever a block of genes with similar sequence and order to a block of genes in chromosome 1 of Tetraodon are found, they are colored dark purple too. So, for instance, we find bits of Tetraodon chromosome 1 scattered throughout our chromosomes 1, 2, 3, 14, and so forth, and Tetraodon chromosome 9 has been broken apart and sprinkled through human chromosomes 1, 2, and largely in 6. By comparing these shattered scraps of chromosomes and assuming the minimal set of operations that must have occurred to create these rearrangements, we can deduce the organization of the ancestral chromosome set of the last common ancestor of Tetraodon and humans. It’s a combination of molecular archaeology and elaborate logic game, and it is impressive intellectual fun.

It’s an approach that has considerable power, too, to let us look back into the genetic state of long extinct organisms, which haven’t left us their actual, intact DNA, but only the somewhat scrambled strands of their descendant’s chromosomes.

Next up: I’ll summarize recent work on the amphioxus genome. Trust me, you need to understand the principle of synteny to see the significance.

I’ve said it before and I’ll say it again… reality rocks SOOO much harder than imaginary friends being responsible for everything. How can you not look at this demonstration of genetics and realize how much more amazing and satisfying it is than “goddidit”?

In math, when we’re looking at the group of transformations of a set of objects, e.g. words in an alphabet like nucleotides in a genome, one of the biggest questions is, “what are the invariants of this transformation?” I never thought of this before, but are those invariants useful structures in this study?

For example, no biologist I, but some of the most common transformations are reversals, swaps, and duplications, right? So I would guess, based on the underlying math, that there are a lot of parts of a large genome that are invariant under such transformations, simply because when such mutations happened to them they wouldn’t be destroyed… though thinkign about it evolutionarily, I suppose there’s not necessarily any erason to select for such structures.

*Are* there long stretches in the genome of structures that survive mutations, such as…

…stretches of DNA on nearby chromosomes that are the same, so that swaps don’t change them?

…stretches of palindromic DNA, which are unchanged under reversals?

…stretches of GGGGGGGG or AAAAAAAA, to which point shifts are mostly irrelevant?

While these structures might not have done much themselves when they arose, as common “library material” they might have been co-opted by other processes and started performing useful functions. Are they there? Are they easy/hard to find; do they say anything about genomic structure?

IIRC, the paper that first pointed this out (in cereals) was rejected by Nature. One of the upshots of that was that they gave up trying to sequence the wheat genome, and used rice instead (it has less junk DNA).

At my undergrad thesis defense, one of my examiners tried to tell me that the chicken was a better model organism than the mouse because chicken chromosomes are more syntenic with human chromosomes. I got to say “but with the mouse you have all the right genes, just not necessarily in the right order”, which made me happy.

So you’re saying god plays cards with life? Or is it that puffer fish can play cards with DNA? No wait, you’re saying that biologists (read:Darwinists) think they’re god and genetically engineer cards to be human-puffer fish hybrids.

No wonder gay marriage is legal and abortions are up. This nation has fallen away from god. You’ve said enough.

(great post PZ. Thank you for taking the time. I love that about this blog. I almost feel like re-visiting a bio class under your instruction.)

In your color-coded example, species 2’s hand #3 is not exactly
like the the non-color coded example above it (after the two
modifications): the 5 and 6 of clubs are swapped. Not sure if
it’s intentional or not, but it means the color-coded example
for species 2 is now the result of *3* changes.

This is Rockin’ with Dokken awesome! It is a powerful teaching tool. I have an idea on how to make it even more powerful a tool. Put this into Flash. Run through the process as given. Then key each card (gene) to a phenotype like hair color, eye color, height, etc. Run the process from the start with the keying.

I will see if a friend of mine who does flash web design and co do this for me. If so it won’t be anytime soon. If someone else can do it please share.

“Pardon my thickness, but how would I know they occurred in that order?”

Deductive reasoning. It’s likely that the inversion of 5-8 occured first, and then part of that inversion was involved in the translocation between hands, which left the initial inversion in tact. That’s the more likely scenario than the translocation of the “cards” between hands happening, and then having 2 inversions take place in the two hands after translocation that resulted in the example shown.

Wow… terrible job of explaining that on my part… that’s why we leave this stuff to PZ… hope it helps anyhow.

I read this blog and a few others (Bad Astronomy) mostly for the social commentary, and to watch you stick it to IDiots and other deserving types. Mostly, your real sciency stuff just sails right over my head.
With this post, I have come closer than ever before to actually understanding one of your serious technical offerings.
Thanks, dood.

It’s quite simply exciting to be able to read about this kind of work. The whole approach reminds me of the methods used by linguistics to try and reconstruct dead languages such as the proto-European ‘mother’ tongue of the majority of the languages spoken by Europeans these days. I wonder how much exchange in terms of methodology has occurred between these disciplines.

This is without a doubt going to be a complete noob question, but it just occured to me now…

When a mutation gets ‘passed on’ to an organism’s offspring, does that imply that the mutation occured in the sex cells of the organism or something? I mean, does the actual location (in the organism) of the mutation play a part in whether it gets passed on?

There are probably people more knowledgable than I groaning and rolling their eyes right now, but I’m working from a secondary school level of biology education here!

Try as I might, I never learn anything here. Just the reverberating echo chamber of Jesus haters in self congratulatory yelps and howls, and “just so stories” and fairy tales for adults. You naturalistic materialists are missing so much of the richness of God’s creation with your reality based lives…

Oh, crap, I’m sorry, I tried to keep a straight Poe but I just couldn’t do it. Thanks PZ, for this entry. Written so well that even a ninnyhammer such as myself can grok.

I’m not sure how often linguists make use of the same vocab (i.e. synteny), but evolutionary principles are often made use of as metaphors or mechanisms (or both) to understand and evaluate language diversification. Many (possibly most) linguists refer the change in languages over time straightforwardly and unabashedly as “language evolution.” See, for example, Salikoko Mufwene’s book The Ecology of Language Evolution, and his paper “Competition and Selection in Language Evolution” in the journal Selection (Vol 3, No 1, Nov 2002).

Thank you Celtic Evolution & Kid Bitzer. Am I correct in understanding that its viewed as the most likely order of events simply due to the fact that the inversion is more simplistic than the translocation? Or have I botched that thought process?

I’m not sure how often linguists make use of the same vocab (i.e. synteny), but evolutionary principles are often made use of as metaphors or mechanisms (or both) to understand and evaluate language diversification. Many (possibly most) linguists refer the change in languages over time straightforwardly and unabashedly as “language evolution.”

Actually, language evolution was accepted (at least by experts) before biological evolution, and the former was used as an analogy for the latter. The similarity in the inferences is hardly escapable.

Many IDiots and creos accept language evolution, but not biological evolution. Which is truly bizarre, considering that for most language evolution there is nothing but “morphlogy” which provides evidence of that evolution, and languages like Indo-European have never been seen in any form at all.

With evolution we have the morphologies, fossils (we have “fossils” for just a few languages–writings in Greek and Latin, for instance), and the DNA which is causally responsible for the fossils (and indeed, is something like text left from earlier times, if changed by varying degrees). Language loses much more evidence during pre-literate times than does biology.

And if any evolution does have some design in it, it is language evolution. Nevertheless, virtually no one tries to claim that God made the language, which has marks of design in it. They prefer to claim that God made biology, which happens to lack the rationality, purpose, and planning found in actual design.

This notion of a relationship between the two evolutions [biological and linguistic] was not about to go away. In early 1863 Charles Lyell published a book on Antiquity of Man that established that humans had been around much longer than the Bible says. In the book he also gave up a long quarrel with Louis Agassiz and agreed that in recent times (by geological standards) there had been a great ice age. (This new position is what Darwin refers to when he mentions the book’s material about glaciers.) Late in the book Lyell also addressed the continuing tangle of analogies between biological, geological, and linguistic change.

Lyell was pleased, when I told him lately that you thought that language might be used as excellent illustration of derivation of species; you will see that he has admirable chapter on this [in Antiquity of Man]. [To Asa Gray; Feb. 23, 1863]

I have read Lyell’s book. The whole certainly struck me as a compilation; but of the highest class, for where possible the facts have been verified on the spot, making it almost an original work. The Glacial chapters seem to me the best, & in parts magnificent. I could hardly judge about Man, as all the gloss of novelty was completely worn off. But certainly the aggregation of the evidence produced a very striking effect on my mind. The Chapter comparing language & changes of species seems most ingenious & interesting. He has showed great skill in picking out salient points in the argument for change of species; but I am deeply disappointed (I do not mean personally) to find that his timidity prevents him giving any judgment. [To Joseph Hooker; Feb. 24, 1863]

Gray, however, was not so impressed.

The Chapter on language makes the points I supposed would be made, or some of them, but only dips in;–leaving more to be said. But this is rather ticklish ground,–for, if we are not careful here, you would get the better of us in this field quoad designs. [From Asa Gray; April 20, 1863]

Darwin loved that last, cryptic remark about designs. Gray believed in evolution, but did also believe that humans had been specially designed. I take his point to be that language evolves without being designed so “we” [supporters of design] had better be careful lest “you” [Darwin] win the argument about design. Darwin spread the news of this remark and elaborated on it, making it sound more pointed than it originally appeared:

That is a clever remark in Gray’s letter about origin of language telling against each trifling variation being designed; Lyell shirked this point, which I urged him to grapple with. I do not believe there are above half-a-dozen real downright believers in modification of Species in all England: certainly not more, who dare speak out. [To Hooker; May 9, 1863]

Anyway, it appears that early on the creationists were having a tough time with the analogy between the two, and with design issues. Nevertheless, they were rather less duplicitous than the current crop of idiots, who largely avoid whatever sinks their claims.

Nevertheless, virtually no one tries to claim that God made the language, which has marks of design in it.

Well, to be fair, many would say that the original language (languages?) were designed by God. Then they might or might not credit God with “confusing languages” at the tower of Babel–but even those who assert the latter are more in tune with the “degeneration” idea than with design of the “confused languages” as such.

Mainly, however, the “high class” creationism, ID, would generally accept language evolution, as do many more traditional creationists.

Hey, cool. I have a gene translocation. I’m a normal phenotype, but the genotype is abnormal. A piece from the end of chromosome 7 is switched with the end of chromosome 11. We only found out because of testing that was done after some miscarriages we experienced. But it explained the long line of miscarriages back through my family tree, and the collapse of family size from a dozen or so to zero, 1 or 2 in a generation.

If my kids got the normal halves of 7 and 11, they will be genotype normal, but if they got the two translocated halves, they are going to be like me, and prone to creating miscarriages at the rate of 50% of pregnancies (the loss of this information on these two genes was lethal to the fetus).

It was kind of cool that we were at a time in history when we were able to get a long standing family mystery resolved.

Beautiful analogy. One question though. You mention that these rearrangements happen very infrequently…. what do you think of the recent phenom of copy number variation? The paper I linked finds 2-5 million base pair insertions in 2/196 control individuals (assumed to be normal people) that do not exist in either parent!!! With that sort of variability being generated I am surprised that we haven’t evolved ESP yet, or at least that you can recognize synteny between us and pufferfish. What are your thoughts?

I am am immunologist, and don’t have a comfortable grasp of what’s going on in that thar nucleus

The paper I linked finds 2-5 million base pair insertions in 2/196 control individuals (assumed to be normal people) that do not exist in either parent!!!

That’s in the repetitive DNA, which is extremely prone to replication mistakes — the polymerase can slip back and forth without noticing, and because most of the repetitive DNA (all long stretches of it) is junk DNA, natural selection doesn’t notice either. In non-repetitive DNA, such mistakes are much rarer.

@Claudia
If you *only* reversed the order, you’d get a different result. Get out a deck of cards and do it. If you first do the reversal, and then the swap, you get the correct result. If you do the swap and then the reversal, you get something different. You’d need more total operations to get to the correct final “genome” if the first move was a swap (you’d need a total of three, and the swap would have to involve a larger section).

When you describe the amphioxus paper, please go into some detail about ascidian development. My wife and I were chatting about this one the other night, and couldn’t really work it out. The sense that I had from the paper was that it was suggesting that ascidians are in some way “degenerate” descendants of some common ancestor of amphioxus and ascidians, but I didn’t have the background about what the ascidian genome or physiology looks like (beyond oooh, pretty sea tulip!) to really understand it.

And what, please, is synteny? Synteny is the conservation of blocks of order within two sets of chromosomes that are being compared….

Actually, in its original usage, “synteny” (syn + teny, literally, “same thread”) simply referred to physical linkage, not order. Two or more genes that are located on the same piece of DNA (thread) are in a syntenic arrangement.

Strictly speaking, then, “conserved synteny” should be used to refer to groups of genes that are linked in one genome whose corresponding versions (orthologs) are also mutually linked in a second genome. But (at least if you follow the original meaning of synteny) here’s no requirement for preservation of order, just linkage.

The situation of “conserved colinearity,” in which a block of genes are found in the same (or nearly the same) order in two genomes, is then a special case of the more general notion of conserved synteny.

Since until the last year or so observations of related genome organization were between relatively “close” genomes (e.g., human and some other mammal, or two species from the same genus of nematode or fly), blocks of conserved colinearity were often found, and these came to be called “syntenic” colloquially.

Between fish and human, however, these conserved blocks of colinear genes are quite short. A striking result of the Tetraodon-human comparison (as shown in the figure above) is that short colinear human-pufferfish gene blocks are still often linked to each other over long stretches but with scrambled block orders. But if you look carefully you’ll see that its wrong to think of the pufferfish-human conserved synteny as large-scale colinearity — the gene order is actually quite scrambled!

One detail of this model seems unlikely to me–I would think that the first few million hands would be played far more loosely–only tending to reproduce the genetic pattern. The mechanism by which the rules are followed would have needed to evolve along with phenotype. Or is the mechanism (given DNA) too foolproof?
It also occurs to me that the more prolific a breeder a species is, the less crucial exact genetic replication might be, especially if faced with a diverse environment.

Hehe Cute. I can’t say evolution is all that hard to understand, but this demonstration is more than explananing, it’s illuminating. Amazing how the tiniest, easiest, simplest change of molecule governed only by physics and chemistry begins the snowball that would become, millions and millions of years later, Ted Haggard. What a waste, huh?

Thanks, PZ,for taking the time and effort to explain this concept at a level even we lurking thickies can understand. (Hyuk hyuk!) I scuttled out of university nearly three decades ago, intellectual tail tucked between my legs, confident in my mouthbreathing inability to grasp any information remotely related to higher education, and yet, you made that seem so clear and simple. It’s almost as if you’re some sort of… magical teaching person!

I’ll bet you could probably make some sort of a career out of gathering students into a room with you and explaining things they don’t yet know!

Owlmirror @ #35, your HTML is on the spot, although for some reason the selected font in the machine I’m working from has no glyph for diamonds (FWIW, Times New Roman does, as well as Arial).

Anyway, PZ probably favoured inline GIFs instead of characters to ensure that everybody would see the proper symbol (which is defering to poor software, but hey).

However, PZ’s GIFs were way below his usual immaculate spotlessnes (pardon the redundancy), as they were kludged from JPG originals, which is a Bad Thing, and there’s even a slightly color shade difference between hearts and diamonds.

Thank you, TB. I think I get it. Because the inversion exists in the translocation ALREADY…and the simplest answer is assumed…right? Instead of assuming it would take the 3 tries to achieve that chromosome, we assume it took the path of least resistance? Oh somebody, please, tell me I’ve gotten it! :((

Seriously, I wanted to post a note of gratitude for your time and effort, PZ, and this offering is the perfect place to do it. My academic background is in anthropology, education, and nonprofit management–notice the lack of any hard science beyond the absolute minimum required for the first degree. Moreover, that absolute minimum came in the form of geology and a single scary chemistry class, with no biology.

All the way back in high school, I did have one biology class. It was taught by the football coach, who bumbled his way through reading us the textbook out loud until he suddenly recognized a word, at which point we spent an entire month learning how to safeguard hunting dogs from the particular worm whose name had been familiar to our teacher.

Yet, I’ve always been interested in reading about the life sciences, and both my kids are planning to major in biology-related fields in college. And, stumbling on your blog a while back has been a wonderful thing for me. The ridiculousness of magical challenges to straightforward science, and the associated political hoopla, provides enough social-science context that my brain contextualizes and files away the biology tidbits themselves painlessly, resulting in an enjoyable, successful educational experience that I didn’t even have to pay tuition to access.

Wow.

Thank you so much for all the loving energy you put into this endeavor. Because of you, some of us mostly-quiet lurkers are better informed, better educated, and better networked than we would otherwise have been. I really appreciate that!

Celtic, #3 — I agree. To draw an analogy, I find the idea of scanning a beam of electrons, the strength of which is continuously being adjusted, over a light-emitting screen so as to produce an image, to be much more fascinating than the idea of there being little people inside the TV.

You forgot the most basic “In the beginning was the Word.” The tower of Babel was after the Fall, one of the consequences of which was the fracturing of human ability to communicate. So, yeah, they’ve got that one covered.

I’m neither a Christian (never was) nor a scientist (although I showed promise as a child). I merely love and recognize the value of lifelong learning. That’s why I’m one of the many non-scientists here who struggle through the more technical posts on this blog, knowing I only understand a fraction of what is being said. To the depths of my comp-lit heart, I appreciate that there are so many talented scientists and science teachers lighting the way. Thanks for communicating with all of us, PZ, not just your peers.

Many IDiots and creos accept language evolution, but not biological evolution.

The literalist Young Earth fundtards who treat Noahs Ark as as an historical event usually take the Tower of Babel story literally as well.

It makes sense in terms of internal logic (loose definition) since no one would imagine such diverse language groups evolving over a six thousand year period.

I always pay attention to that because it was the ‘Noah’s Ark’ and ‘Tower of Babel’ stories that convinced me religion was a pathetic attempt at explaining anything, only a moron would believe such crap, and they are lying to me in order to coerce certain behaviors.

I was 7 years old and have functioned as an Atheist ever since.

This exact experience is fairly common BTW. I refer to us as the ‘quick learner’ Atheists.

“not every generation and not even every speciation event is accompanied by an error”

Shouldn’t that be the other way round? I was under the impression (sorry no biology in my background) that every speciation would have to be the result of a combination of an accumulation of errors providing an advantage to a changed environment (or have I been reading Gould too much?)

I also remember reading somewhere that mutational errors – mostly having no effect at all – occur at a pretty high rate, 1.6 changes per generation was the figure I remember.

Lastly I realize its not your purpose here – and might detract from your point – but perhaps throwing in a comment about sexual exchange at the end might be useful.